1,720,957 research outputs found
Towards pocket-sized genomic analyses: cross-platform benchmark of multi-organism genomic data indexing and alignment
Full text linkThe current socio-economic situation as well as international objectives set by the United Nation (2030 Sustainable Agenda) underline the urgency of low-cost and environmental-friendly computational alternatives. Moreover, in recent years the bioinformatic community has shown renewed interest for Raspberry Pi (RPi) application in teaching and research projects. In the context of the BioVRPi project - which aims to develop and offer a low-cost, stable and tested bioinformatic environment - we propose an exploratory cross-platform benchmarking of multi-organism genomic analyses. The benchmark of indexing and alignment processes was carried out on the following devices: RPi 4 (Raspberry Pi OS 04-04-2022) RAM 8GB HDD storage, laptop (MacOS Big Sur v11.2.3) Intel Core i5 2GHz quad-core processor RAM 16GB SSD, and desktop (Ubuntu 20.04.4 LTS) Intel Core i7 3GHz octa-core processor RAM 32GB HDD storage. Performance assessment was evaluated on SARS-CoV-2 virus, Escherichia coli and Caenorhabditis elegans genome sequences (respective RefSeq accessions: GCF_009858895.2, GCF_000005845.2, GCF_000002985.6) since they present different degrees of genomic complexity: virus, bacterium, and nematode. To minimize variability and possible biases due to sequencing technologies used, sample reads were generated in silico from their respective reference genomes using ART Illumina v2.5.8 with the following parameters: read length 150, paired end, coverage 30X, mean fragment length 200, standard deviation 10, HiSeqX v2.5 TruSeq built-in profile. Indexing and alignment were performed with 3 alignment tools: BWA v0.7.17-r1188, Bowtie2 v2.4.5, and Minimap2 v2.17, using default parameters and scaling from 1 up to 4 threads. Benchmarking was evaluated using Hyperfine v1.13.0 with a warmup step of 3 simulations and 10 runs for each process. We performed a cross-platform benchmark of multi-organism genomic indexing and short reads alignment to evaluate RPi as a viable alternative to common bioinformatic devices. To assess its performance, we tested some of the most widely used alignment tools on SARS-CoV-2, E. coli and C. elegans genomic data (respective genome sizes: 29.9Kbp, 4.6Mbp, 100.3Mbp). The computational times for indexing and alignment are reported in Table 1. As regards indexing, we observed comparable runtimes among RPi and other platforms using BWA and Bowtie2 for SARS-CoV-2 and E. coli, whereas Minimap2 indexing showed an increase of one order of magnitude in runtimes for RPi. Nonetheless, Minimap2 showed the fastest runtimes for indexing overall. In addition, we found an increase of one order of magnitude in RPi runtimes for C. elegans for all considered tools, even though differences in runtimes across platforms showed to be stable across organisms. As regards the alignment process, we observed consistency in runtimes differences across all organisms and tools. Overall, Minimap2 performances proved to be the fastest whereas Bowtie2 displayed poor performances across all platforms, exacerbating its inefficiency on RPi. Even though BWA seems to work more efficiently on RPi than on desktop for SARS-COV-2 data, desktop and laptop showed better performances on more complex organisms as expected. Benchmarking analyses considered multi-threading up to 4 threads, the maximum available on RPi. As regards indexing on Bowtie2, multi-threading proved to be effective for C. elegans data, showing no improvement in runtimes for SARS-CoV-2 and E. coli. Conversely, alignment showed the best performances using multi-threading as expected. In conclusion, RPi showed promising results, proved to be a viable low-cost and environmental-friendly alternative to perform genomic data analysis on different organisms and turned out to be particularly efficient for microorganisms. Further advances and tools optimization for RPi ARM architecture will lead to a greater scalability for complex organisms and will be carried out by the BioVRPi project in future exploratory analyses
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Shewanella algae and Vibrio spp. strains isolated in Italian aquaculture farms are reservoirs of antibiotic resistant genes that might constitute a risk for human health
No full textThe aquatic environment can represent a reservoir of antimicrobial resistance genes. In the present study, phenotypical, biochemical and molecular techniques were used to screen a collection of marine strains isolated in Italian aquaculture farms to investigate their beta-lactam resistance profiles. The genome of 12 carbapenemase and/or beta-lactamase producing strains was sequenced and a phylogenetic analysis of the beta-lactamases found in their chromosomes was performed. Gene annotation and prediction revealed the presence of blaAmpC and blaOXA-55-like in all the Shewanella algae isolates whereas in Vibrio anguillarum and Vibrio parahaemolyticus strains, blaAmpC and blaCARB-19 were found, respectively. Multiple alignments of OXA-55-like and AmpC protein sequences showed different point mutations. Finally, comparisons between enzyme phylogeny and strain clusterization based on sampling sites and dates indicate the diffusion of specific Multi Drug Resistant (MDR) Shewanella algae clones along the Italian Adriatic coast
P139 Hypermutation as an evolutionary mechanism for Achromobacter spp. in cystic fibrosis lung infection
No full textObjectives: Achromobacter spp. can cause chronic infections in the lungs of CF patients. One of the main mechanisms favouring the persistence of CF pathogens is hypermutation, in which defects in DNA repair processes promote an increased DNA mutation rate. In this study, longitudinal isolates were screened to verify the occurrence of hypermutators. Methods: 34 Achromobacter spp. clinical isolates were longitudinally collected over 3 years from 10 patients (CF Center of Verona, Italy) and underwent whole genome sequencing. Phylogenetic and variant analyses were performed. Presence of high impact mutations in mismatch repair (MMR) system genes, transition/transversion (ts/tv) ratio >3 and variant rate >3 were arbitrarily defined as criteria for hypermutation. Results: According to sequencing and phylogenetic analyses, 3 species of Achromobacter spp. were identified: A. xylosoxidans (25 isolates, 7 patients), A. rhulandii (4 isolates, 1 patient) and A. insuavis (5 isolates, 2 patients). MMR genes analysis showed that all A. rhulandii and A. insuavis genomes presented 2 copies of mutS gene while a single copy was detected in A. xylosoxidans genomes. Regardless of the species and number of mutS gene copies, 21 isolates (7 patients) overall were identified as hypermutators: they presented high impact mutations in either mutS, mutL, or mutT, high ts/tv ratio and increased mean yearly variant rate. Conclusions: Most of the enrolled patients (70%) with chronic infection presented hypermutators strains. Such a high prevalence confirms the occurrence and importance of hypermutation as an adaptive mechanism in Achromobacter spp. infection. Hypermutation could potentially influence the clinical outcomes and the efficacy of treatments, highlighting the need to clarify its impact in order to develop appropriate therapeutic regimens. Acknowledgments: This study was supported by the Italian CF Research Foundation (project FFC#18/2019)
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Dispelling the Myths Behind First-author Citation Counts
Full text linkWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
koamabayili/VECTRON-author-checklist: VECTRON author checklist
No full textWe have done our best to complete the author checklist relating to the use of animals in the hut study. Note that the objective for the hut study was to evaluate the IRS treatment applications for residual efficacy against Anopheles mosquitoes, including the local An. coluzzii mosquito population. Cows were only used to attract mosquitoes into the huts and no tests were carried out directly on the cows. The author checklist is intended for use with studies where experiments are carried out on animals, which is why we have had such difficulty in completing this for the hut study, as many of the questions do not relate to how the cows were used
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